From jbrown@iris7.carb.nist.gov Thu Jan 5 00:33:54 1995 Received: from ENH.NIST.GOV for jbrown@iris7.carb.nist.gov by www.ccl.net (8.6.9/930601.1506) id XAA11300; Wed, 4 Jan 1995 23:50:51 -0500 Received: from iris7.carb.nist.gov by ENH.NIST.GOV (PMDF V4.2-13 #4653) id <01HLGTJVQ54G0025KW@ENH.NIST.GOV>; Wed, 4 Jan 1995 23:49:35 EST Received: by iris7.carb.nist.gov (920330.SGI/920502.SGI) for @enh.nist.gov:chemistry@ccl.net id AA03016; Wed, 4 Jan 95 23:51:45 -0500 Date: Wed, 4 Jan 1995 23:51:45 +30000 From: James Brown Subject: MOPAC for Macintosh... To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Subject says it...is it available? Maybe even for the Power Mac? If not, any ideas on how to go about compiling it? Regards, James Brown Center for Advanced Research in Biotechnology From ibi@translell.tutkie.tut.ac.jp Thu Jan 5 02:33:58 1995 Received: from translell.translell.tutkie.tut.ac.jp for ibi@translell.tutkie.tut.ac.jp by www.ccl.net (8.6.9/930601.1506) id CAA12257; Thu, 5 Jan 1995 02:29:53 -0500 Received: (from ibi@localhost) by translell.translell.tutkie.tut.ac.jp (8.6.9+2.4Wb3/3.3Wb) id QAA01032 for CHEMISTRY@ccl.net; Thu, 5 Jan 1995 16:30:39 +0900 Date: Thu, 5 Jan 1995 16:30:39 +0900 From: Ibi Deretey Message-Id: <199501050730.QAA01032@translell.translell.tutkie.tut.ac.jp> To: CHEMISTRY@ccl.net Subject: HELP Dear Netters: Could anyone of you share a piece of program to compute hydrogen coordinates for a molecule whose crystalographic data is known? Perhaps a FTP site where this program is available? Thanks in advance: Ibi From mirko@sara.nl Thu Jan 5 04:33:58 1995 Received: from vax3.sara.nl for mirko@sara.nl by www.ccl.net (8.6.9/930601.1506) id DAA13007; Thu, 5 Jan 1995 03:54:37 -0500 From: Received: from horus.sara.nl by SARA.NL (PMDF V4.2-15 #2498) id <01HLHEQMBB349QV3EF@SARA.NL>; Thu, 5 Jan 1995 09:55:56 +0100 (MET) Received: by horus.sara.nl (AIX 3.2/UCB 5.64/4.03) id AA111674; Thu, 5 Jan 1995 09:54:20 +0100 Date: Thu, 05 Jan 1995 09:54:20 +0100 Subject: Re: CCL:MOPAC for Macintosh... To: chemistry@ccl.net, jbrown@iris7.carb.nist.gov Message-id: <9501050854.AA111674@horus.sara.nl> X-Envelope-to: chemistry@ccl.net Content-transfer-encoding: 7BIT There is definitely MOPAC available for a (Power) Mac. We are currently using a CAChe Worksystem, which is a suite of comp. chem applications, including MOPAC. We use a PowerMac 950, equipped with additional CAChe coprocessors, but the software also runs on simple Macs (small systems only). Prices and so on: CAChe Scientific fax: 503-531-1899 (USA) tel: 503-531-1804 Good luck, Mirko Kranenburg University of Amsterdam Dept of Inorganic Chemistry and Homogeneous Catalysis e-mail: mirko@sara.nl PS. I'm not associated with CAChe, just an enthousiastic user. From CHMIGORN@NUSVM.NUS.SG Thu Jan 5 05:34:00 1995 Received: from phem3 for CHMIGORN@NUSVM.NUS.SG by www.ccl.net (8.6.9/930601.1506) id FAA13433; Thu, 5 Jan 1995 05:22:23 -0500 Received: from NUSVM.NUS.SG (MAILER@NUSVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HLH56DMFPS94HZKH@phem3.acs.ohio-state.edu>; Thu, 5 Jan 1995 05:22:18 EDT Received: from NUSVM.NUS.SG (NJE origin CHMIGORN@NUSVM) by NUSVM.NUS.SG (LMail V1.2a/1.8a) with RFC822 id 3406; Thu, 5 Jan 1995 18:02:42 +0800 Date: Thu, 05 Jan 1995 17:58:49 +0700 (SST) From: "I.Novak" Subject: MAPLE V RELEASE 3 To: CHEMISTRY@ccl.net Message-id: <01HLH56DMFPU94HZKH@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Dear netters, I have a question concerning programming in Maple V. I generate a pair of real numbers in each cycle of a certain loop. Which algorithm should I use in order to plot all the pairs thus obtained on a single 2D graph. I have tried plot etc but it does not work. print(x,y); prints the pairs correctly on the screen, so my wish is to be able to represent them graphically. Thanks! Dr I.Novak,Dept.of Chemistry,National University of Singapore,Singapore 0511,Singapore bitnet: chmigorn@nusvm internet: chmigorn@nus.sg From Patrick.Bultinck@rug.ac.be Thu Jan 5 05:37:23 1995 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id FAA13461; Thu, 5 Jan 1995 05:25:30 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA19612 (5.67b/IDA-1.5 for ); Thu, 5 Jan 1995 11:24:34 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA18015; Thu, 5 Jan 1995 11:25:02 +0100 Date: Thu, 5 Jan 1995 11:25:02 +0100 (MET) From: Patrick Bultinck To: "comp. chem. list" Subject: RIOS or PPC for new RS/6000 ? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 620 Dear, I am trying to get some funds to be able to buy a new RS/6000 for the research group I'm in. I want to keep using RS/6000, but here's an important question I'd like to get a second opinion on. I have to do a LOT of integrating, matrix handling etc., and I would like to know what you would prefer to buy for an amount of x dollars : A PowerPC based machine that could be upgraded to let's say a 604 by Sept. or A RIOS(2?) based machine, like 3AT. I'd like to go for the second one, but would like to know what more experienced people think ! Thanks a lot !! Patrick Bultinck, University of Ghent, Belgium From ANWAR@vms.huji.ac.il Thu Jan 5 05:40:40 1995 Received: from VMS.HUJI.AC.IL for ANWAR@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id EAA13315; Thu, 5 Jan 1995 04:59:26 -0500 Received: by HUJIVMS (HUyMail-V7a); Thu, 05 Jan 95 11:59:29 +0200 Received: by HUJIVMS (HUyMail-V7a); Thu, 05 Jan 95 11:58:40 +0200 Date: Thu, 5 Jan 95 11:58 +0200 Message-id: <05010095115835@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: summary Dear Netters, Thank you for your answers to my question concerning the stability of tetrahedral intermediates. These are the answers: ***************************************************************************** From: "E. Lewars" To: anwar@vms.huji.ac.il Subject: TETRAHEDRAL INTERMEDIATES See J. L. Wilbur and J. I. Brauman, J. Am. Chem. Soc., 1994, 116, 9216-9221. === ***************************************************************************** From: carl@biosym.com (Carl Ewig) To: anwar@vms.huji.ac.il Subject: tetrahedral intermediates Anwar, See: C.S.Ewig and J.R. Van Wazer, J.Am.Chem.Soc. 108, 4774-4783 (1986). Regards, Carl Ewig ***************************************************************************** Thanks a lot for your responses. anwar rayan anwar@vms.huji.ac.il From ANWAR@vms.huji.ac.il Thu Jan 5 06:34:00 1995 Received: from VMS.HUJI.AC.IL for ANWAR@vms.huji.ac.il by www.ccl.net (8.6.9/930601.1506) id GAA13994; Thu, 5 Jan 1995 06:19:42 -0500 Received: by HUJIVMS (HUyMail-V7a); Thu, 05 Jan 95 13:19:44 +0200 Received: by HUJIVMS (HUyMail-V7a); Thu, 05 Jan 95 13:06:14 +0200 Date: Thu, 5 Jan 95 13:06 +0200 Message-id: <05010095130606@HUJIVMS> From: To: chemistry@ccl.net, ibi@translell.tutkie.tut.ac.jp MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: hydrogen coordinates Dear Netteres, Ibi Deretey wrote: ***************************************************************************** Dear Netters: Could anyone of you share a piece of program to compute hydrogen coordinates for a molecule whose crystalographic data is known? Perhaps a FTP site where this program is available? Thanks in advance: Ibi ***************************************************************************** You have not mensioned the size of the molecule. you may add the hydrogen atoms by INSIGHT (interactive molecular graphics program) (Biosym Inc.). if the molecule is bigger than 200 atoms you have to use molecular mechanics programs (like DISCOVER) to optimize positions of hydrogen atoms. if the molecule is less than 200 atoms you may use one of the semiempirecal methods. MNDO/H produce good geometric results and describe well hydrogen-bonding. for further details see: Jesus Rodriguez, Journal of Computational Chemistry, Vol.15, No.2,183-189 (1994) The program of MNDO/H you may recieve from Prof. A. Goldblum from the Hebrew University of Jerusalem. his E-mail: amiram@vms.huji.ac.il By the way, if your molecule is somehow big and you still have special interest in positioning hydrogen atoms correctly, you may cut the system to pieces. Hoping that this will help you. with best wishs anwar rayan anwar@vms.huji.ac.il From ccl@ccl.net Thu Jan 5 11:17:54 1995 Received: for ccl@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA17951; Thu, 5 Jan 1995 11:17:54 -0500 Date: Thu, 5 Jan 1995 11:17:54 -0500 From: Computational Chemistry Message-Id: <199501051617.LAA17951@www.ccl.net> To: chemistry@itp.chg.free.net Subject: Comp-Chem-List I am a coordinator of the Computational Chemistry List. The mail is bouncing from your address chemistry@itp.chg.free.net and I have to unsubscribe you from the Computational Chemistry List. Hoping that the network problems will be resolved soon at your site, I invite you to resubscribe at that time by sending me a short note to the address: chemistry-request@ccl.net Thank you for participating. Jan Labanowski Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43212-1163 ph. 614-292-9279, FAX: 614-292-7168 E-mail: jkl@ccl.net or JKL@OHSTPY.BITNET From mbass@amgen.com Thu Jan 5 11:34:15 1995 Received: from relay1.UU.NET for mbass@amgen.com by www.ccl.net (8.6.9/930601.1506) id LAA18780; Thu, 5 Jan 1995 11:33:21 -0500 Received: from amgen.com by relay1.UU.NET with SMTP id QQxxju23492; Thu, 5 Jan 1995 11:31:22 -0500 Received: from ichthyo.amgen.com by amgen.com (5.0/SMI-SVR4) id AA17643; Thu, 5 Jan 1995 08:31:25 -0800 Received: by ichthyo.amgen.com (931110.SGI/911001.SGI) for @amgen.com:chemistry@ccl.net id AA09260; Thu, 5 Jan 95 08:30:21 -0800 Date: Thu, 5 Jan 95 08:30:21 -0800 From: mbass@amgen.com (Michael Bass) Message-Id: <9501051630.AA09260@ichthyo.amgen.com> To: ANWAR@vms.huji.ac.il Cc: chemistry@ccl.net, ibi@translell.tutkie.tut.ac.jp In-Reply-To: <05010095130606@HUJIVMS> (ANWAR@vms.huji.ac.il) Subject: Re: CCL:hydrogen coordinates content-length: 1284 Date: Thu, 5 Jan 95 13:06 +0200 From: Sender: Computational Chemistry List [...] You have not mensioned the size of the molecule. you may add the hydrogen atoms by INSIGHT (interactive molecular graphics program) (Biosym Inc.). if the molecule is bigger than 200 atoms you have to use molecular mechanics programs (like DISCOVER) to optimize positions of hydrogen atoms. if the molecule is less than 200 atoms you may use one of the semiempirecal methods. MNDO/H produce good geometric results and describe well hydrogen-bonding. for further details see: Jesus Rodriguez, Journal of Computational Chemistry, Vol.15, No.2,183-189 (1994) Another method you might want to look at for optimizing hydrogen position is NETWORK. This program positions the polar hydrogens in a protein structure to form the largest number of possible hydrogen bonds. It also also tries to figure out which nitrogen on histidyl residues the hydrogen should go on. The details are in Bass et al., Proteins 12:266-277 (1992). Michael B. Bass, Ph.D. Amgen, Inc. Mail Stop 14-1-B-239 1840 DeHavilland Drive Thousand Oaks, CA 91320-1789 Phone: (805) 447-1812 Fax: (805) 447-1982 Email: mbass@amgen.com From bonvoisi@cemes.cemes.fr Thu Jan 5 12:34:03 1995 Received: from cix.cict.fr for bonvoisi@cemes.cemes.fr by www.ccl.net (8.6.9/930601.1506) id MAA19828; Thu, 5 Jan 1995 12:09:44 -0500 Received: from cemes.cemes.fr by cix.cict.fr; Thu, 5 Jan 95 18:13:57 +0100 Received: by cemes.cemes.fr; Thu, 5 Jan 95 18:07:16 EST From: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques) Message-Id: <9501051707.AA02087@cemes.cemes.fr> Subject: PSI88 Molecular Orbital To: chemistry@ccl.net (CCL Computational Chemistry) Date: Thu, 5 Jan 95 18:07:14 EST X-Mailer: ELM [version 2.3 PL11] ******* Drawings of Molecular Orbital *************************** This is about free and ftp'able program able to draw molecular orbitals issued from MOPAC type calculations. The other requirement was the ability of working on a RS6000 workstation... Lot of people asked me about the ftp adress of PSI88, It is rani.chem.yale.edu or 130.132.25.65. You can also ask to the author; Dr Daniel Severance at dan@sage.syntex.com Finally, this program works well even for big molecule as soon as you modify the dimension of IB and IC in psi2.f. By increasing the dimension up to 100 instead of the original value ie 35, everything is OK. Thanks to everybody. -- +----------------------------------------------------------------+ | Jacques BONVOISIN | | CNRS/CEMES-LOE Tel : +33 62 25 78 52 | | 29 , rue Jeanne Marvig Fax : +33 62 25 79 99 | | F-31055 Toulouse Cedex Email: bonvoisi@cemes.fr | +----------------------------------------------------------------+ From Karl.F.Moschner@urlus.sprint.com Thu Jan 5 12:46:31 1995 Received: from sprintf.merit.edu for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.9/930601.1506) id MAA19696; Thu, 5 Jan 1995 12:05:06 -0500 X400-Received: by mta merit in /PRMD=internet/ADMD=telemail/C=us/; Relayed; Thu, 5 Jan 1995 09:03:04 -0500 X400-Received: by /ADMD=TELEMAIL/C=US/; Relayed; Thu, 5 Jan 1995 08:57:21 -0500 X400-Received: by /PRMD=SMXFL2/ADMD=TELEMAIL/C=US/; Relayed; Thu, 5 Jan 1995 09:02:12 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 5 Jan 1995 09:02:00 -0500 Date: Thu, 5 Jan 1995 09:02:00 -0500 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Thu Jan 5 09:02:02 199502] X400-Content-Type: P2-1984 (2) Content-Identifier: Reply - Large Ga From: Karl.F.Moschner@urlus.sprint.com Message-ID: <"Thu Jan 5 09:02:02 199502*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: CHEMISTRY@ccl.net Subject: Reply - Large Gaussian RWF Files > I have a question concerning the case of large RWF-files in Gaussian 92/DFT. > Doing analytical FREQ calculations the RWF-file grows to remarkable size and > sometimes becomes larger than the available diskspace (or the limit of the > file-system specified by the operating system). > > Im am working on a AIX-system and I am thinking about the possibility to > split the RWF-file in two files and to put them on two different > file-systems. So my question is, if this splitting of the RWF-file is > possible (and HOW) ? > > But I would also be happy to get other comments on the possibility to > decrease the amount of necessary diskspace during analytical FREQ > calculations. > > Thanx in advance > > Ch. Ehrendorfer Common "workstation" UNIX operating systems (IBM AIX, SGI Irix 5.2 and 6.0, and HP UX but not DEC OSF/1 - nor Cray UNICOS or Convex) limit file system size to about 8-14 GB and a single file to about 2 GB. To minimize Gaussin 92/DFT scratch file sizes, try a combination of the keywords: Direct MP2=Stingy Opt=CalcHFFC Freq=NoRaman This forces direct MP2 and direct SCF which minimizes scratch file size. A system of about 165 basis functions may be accommodated within 2 GB. Using "Freq" without the "NoRaman" modifier reduces the maximum problem size to about 150 basis functions. NOTE: Do not use "Direct" redundantly, i.e., as a keyword AND as a modifier for another keyword since it can "confuse" the job setup routine. For example: DON'T USE THE COMBINATION: Direct Opt=(Direct, CalcHFFC) Modifying the code in order to parse the scratch file(s) is a significant undertaking and may be unneccessary. Relief may be forthcoming in the near future from the eagerly awaited next major update to Gaussian/DFT and manufacturers are bound to introduce changes to their OS in 95-96. In other words, the modified code will be obsolete just about the time you modify and test it. If you really need it now, you may consider purchasing or borrowing time on an alternative system, e.g., DEC OSF/1, which doesn't have this limitation. Karl F. Moschner Karl.F.Moschner@urlus.sprint.com Unilever Research U. S. From TAPASKAR@SIUCVMB.SIU.EDU Thu Jan 5 17:34:07 1995 Received: from SIUCVMB.SIU.EDU for TAPASKAR@SIUCVMB.SIU.EDU by www.ccl.net (8.6.9/930601.1506) id QAA25988; Thu, 5 Jan 1995 16:43:29 -0500 Message-Id: <199501052143.QAA25988@www.ccl.net> Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 7147; Thu, 05 Jan 95 15:41:52 CST Date: Thu, 5 Jan 95 15:41:51 CST From: "Tapas Kar" To: chemistry@ccl.net Subject: Include my email add. in the list. I am interested to receive emails from chemistry-request. Please include my email add. tapaskar@siucvmb.siu.edu in your list. Thanks, Tapas Kar From garlima@if.usp.br Thu Jan 5 18:34:08 1995 Received: from USPIF.IF.USP.BR for garlima@if.usp.br by www.ccl.net (8.6.9/930601.1506) id SAA27476; Thu, 5 Jan 1995 18:18:01 -0500 From: Received: by if.usp.br (MX V4.1 VAX) id 1; Thu, 05 Jan 1995 21:19:45 GMT-03:00 Date: Thu, 05 Jan 1995 21:19:44 GMT-03:00 To: CHEMISTRY@ccl.net Message-ID: <0098A06A.86E2AE80.1@if.usp.br> Subject: concurrent C software Dear Netters, Is there a public-domain compiler called " Concurrent C " If so, please give me any direction of possible site where I can access via ftp. Thanks in advance, G.A.R.Lima Any replay should be send to garlima@if.usp.br ************************************************************************* From garlima@if.usp.br Thu Jan 5 18:44:11 1995 Received: from USPIF.IF.USP.BR for garlima@if.usp.br by www.ccl.net (8.6.9/930601.1506) id SAA27399; Thu, 5 Jan 1995 18:08:47 -0500 From: Received: by if.usp.br (MX V4.1 VAX) id 10; Thu, 05 Jan 1995 21:10:24 GMT-03:00 Date: Thu, 05 Jan 1995 21:10:23 GMT-03:00 To: CHEMISTRY@ccl.net Message-ID: <0098A069.38531940.10@if.usp.br> Subject: looking for COSMO references Dear netters, I am looking for references concerned with applications of COSMO ( Conducting-like Screening Model) in molecular problems. Any references concerned with its methodology are welcome. I will summarize the replays to the CCL, Any advice and pointers to reference are also welcome Thanks! Thanks in advance, G.A.R.lima REPLAYS SHOULD BE SENDED TO ----> garlima@if.usp.br ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From ldw@pchindigo2.IPC.PKU.EDU.CN Thu Jan 5 22:34:10 1995 Received: from pchindigo2.IPC.PKU.EDU.CN for ldw@pchindigo2.IPC.PKU.EDU.CN by www.ccl.net (8.6.9/930601.1506) id WAA29631; Thu, 5 Jan 1995 22:28:35 -0500 Received: by pchindigo2.IPC.PKU.EDU.CN (920330.SGI/911001.SGI) for chemistry@ccl.net id AA02716; Wed, 6 Jul 94 11:16:28 +0800 Date: Wed, 6 Jul 1994 11:16:27 +0800 (SST) From: Lin Dawei X-Sender: ldw@pchindigo2.IPC.PKU.EDU.CN To: chemistry@ccl.net Subject: summary of recent_reviews Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Here is a summary of responses to my question on finding recent reviews of Simulated annealing, Molecular Dynamics, Molecular Mechanics, Monte Carlo Methos. Thank all responsers for their kind and generous help. ------------------------------------------------------------------- Dawei LIN Room 115, Building 27 Peking University Beijing 100871 Doctoral Candidate of P.R.China(Prefered add.) Chemistry Department ldw@pchindigo2.ipc.pku.edu.cn Dawei LIN (86)-1-2501490 tel Institute of Physical Chemistry (86)-1-2501725 fax Peking University Beijing 100871 P.R.China -------------------------------------------------------------------- ******************************************************************************* From: mwd@alamos.cray.com (Mark Dalton) Dawei, For Simulated Annealing or Adaptive Simulated Annealing, by Lester Ingber, you can look at: http://alumni.caltech.edu/~ingber/ There are papers and Adaptive Simulated Annealing software. I hope this is part of what you were looking for. Mark ______________________________________________________________________ Mark Dalton CH3-S-CH2 H H O H Cray Research,Inc. | | | \ | Los Alamos,NM 87544 CH2-C-COO //\ ---C--CH2-C-COO C-CH2-C-COO mwd@cray.com | | || || | // | NH3 \\/ \ / CH NH3 O NH3 NH URL = http://lenti.med.umn.edu/~mwd/mwd.html ______________________________________________________________________ ******************************************************************************** From: tomic@olimp.irb.hr Hello Dawei, Journal for Comp. Chem. and Amer Chem Soc. are the best journals to find relevant papers. Also there are very good book Rew. in Comp. Chem. (Boyd& Lipk.)Sanja ******************************************************************************** From: Lipkowitz Dr. Lin, I have been editing a review series called Reviews in Computational Chemistry" for the past few years. This series covers all topics in computational chemistry and molecular modeling. It is written for novice computational chemists ( approximate level is first year graduate student). We direct the reviews to the experimentalist rather than the theoretical chemist. We have already published 5 volumes and number 6 will be available next month. The series is published by VCH Publishers Inc., New York. I am sending you information via surface mail. Good luck, Kenny Lipkowitz ****************************************************************************** From singer@mps.ohio-state.edu I just wrote a review article on simulated annealing methods for mixed quantum/classical (including Car-Parrinello type) molecular dynamics simulations. The article will appear in a review volume entitled "Applications of Simulated Annealing in Chemistry" to be published by Elsevier. --- Sherwin Singer internet: singer@mps.ohio-state.edu Dept. of Chemistry bitnet: singer@ohstpy Ohio State University (614)292-8909 FAX: (614)292-1685 **************************************************************************** From: blonski@alumina.rutgers.edu (Slawomir Blonski) Some time ago the following message was posted on CCL. Slawomir Blonski __________________________________________________________________ To whom who are interested in Monte Carlo simulation of solutions! Let me turn your attention to our review I. I. Sheykhet and B. Ya. Simkin "Monte Carlo Method in the Theory of Solutions" Computer Physics Reports, 12 (3) 67-133 (1990). I believe it is a good addition to the book of Allen and Tildsley. Below is the content for your convenience: 1. Introduction 2. The Monte Carlo method 3. The problem of ergodicity in the Monte Carlo method 4. Convergence of results 4.1. Criteria for achievment of convergence 4.2. Schemes for speeding up convergence 5. Boundary models, their distinguishing features and effects 5.1. Periodic boundary conditions. Cutting off the intermolecular interaction potentials 5.2. The shortcomings of the periodic boundary conditions 5.3. Free boundary conditions - the cluster approach 5.4. A boundary model in the form of a pure solvent 6. Calculation of the free energy 6.1. The perturbation method 6.2. Thermodynamic integration method 6.3. Umbrella sampling 6.4. Test particle method 7. Methods for approximating intermolecular interaction energies by analytical functions 7.1. The main techniques of approximating intermolecular interactions 7.2. Empirical methods for constructing the potentials 7.3. Non-empirical (ab-initio) methods for constructing the potentials 7.4. Semi-empirical methods for constructing the potentials 7.5. Inclusion of many-body contributions 8. Conclusion References Incidentally, our with Dr. I. Sheykhet book "Quantum Chemical and Statistical Theory of Solutions. A Computaional Approach" will be published in the beginning of the next year by Ellis-Horwood Publishing House, England. Later I will send the content of the book. Best regards Professor Boris Simkin, Department of Chemistry, Cornell University ******************************************************************************* From: lijian@scripps.edu (Jian Li) Hi Dawei, It is nice to see the post from China, especially from the school I graduated from. Concerning your question, you can find a lot of review papers pertinent to the subjects you mentioned if you have a look at: (1) Ann. Rev. Biophys. Biophys. Chem. (2) Curr. Opin. Struct. Biol. In addition, from a recent review by Charles Brooks and Dave Case, Chem. Rev. 93 (1993) 2487, you can trace back to some other useful references. Best regards and happy new year! Jian Li Molecular Biology, MB 1 The Scripps Research Institute La Jolla, CA 92037 ************************************************************************ Some one also kindly send me some recent literatures index(400k). If anyone is interested in it. I'd like forward it to you. ************************************************************************ THE END From ipcakc@vigyan.iisc.ernet.in Thu Jan 5 23:34:17 1995 Received: from sangam.ncst.ernet.in for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id XAA29945; Thu, 5 Jan 1995 23:00:29 -0500 From: Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id JAA16781 for ; Fri, 6 Jan 1995 09:30:04 +0500 Received: from vigyan.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id JAA00423 for ; Fri, 6 Jan 1995 09:27:18 +0530 Received: by vigyan.iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA18113; Fri, 6 Jan 95 09:32:40 EST Date: Fri, 6 Jan 95 09:32:40 EST Message-Id: <9501061432.AA18113@vigyan.iisc.ernet.in> To: CHEMISTRY@ccl.net Subject: eht Dear netters i am interested in doing some EHT calculations on diamond , graphite and their hybrids. i would like to know whether any EHT program is available and whether i can have an access. Kindly let me know the ftp site. thanking you. sumathy. From mei@atlas.rc.m-kasei.co.jp Thu Jan 5 23:35:47 1995 Received: from frontier.m-kasei.co.jp for mei@atlas.rc.m-kasei.co.jp by www.ccl.net (8.6.9/930601.1506) id XAA00864; Thu, 5 Jan 1995 23:25:37 -0500 Received: from atlas.rc.m-kasei.co.jp (atlas.rc.m-kasei.co.jp [133.251.253.2]) by frontier.m-kasei.co.jp (8.6.8+2.4Wb/3.3Wb-m-kasei) with SMTP id NAA15424; Fri, 6 Jan 1995 13:22:24 +0900 Received: by atlas.rc.m-kasei.co.jp (4.1/6.4J.6) id AA17518; Fri, 6 Jan 95 13:19:09 JST From: mei@atlas.rc.m-kasei.co.jp (Akinori MURAKAMI) Message-Id: <9501060419.AA17518@atlas.rc.m-kasei.co.jp> To: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Cc: chemistry@ccl.net, mei@atlas.rc.m-kasei.co.jp Subject: Re: CCL:What makes Gaussian fast ? In-Reply-To: Your message of Wed, 04 Jan 95 11:42:29 +0100. <9501041042.AA25886@tci002.uibk.ac.at> Date: Fri, 06 Jan 95 13:19:09 +0900 Dear Teerakiat Kerdcharoen >> Dear cyber-chemists, ??? >> I have experienced using both GAMESS and Gaussian 92 on >> AIX platform. Gaussian 92 always runs faster than GAMESS in >> most case. I have found on a review article where written Gaussian >> spend the computation at the cost of N**2.7 not N**4 as >> conventional Hartree-Fock scheme (N = no. of Gaussian primitives). That is not true for conventional method. There are only small amount of nonzero integrals(greater than 10**(-10)) and number of those scale as N**(2-3). N**4 is formal scaling not real time computation. cf. R. Ahlichs, Theor. Chim. Acta. vol 33, p157, (1974) >> Which special algorithms are tailored into Gaussian ? Most integral are evaluated by HP(axis rotation method) in both Gaussian and HONDO(GAMESS). Some integrals are evaluated by HGP and PRISM in Gaussian is faster than Rys method in HONDO(GAMESS0. I think that is not main difference. Gaussian seems clever selection for integral evaluation. I don't know the paper. You can imagine from the original paper on direct SCF, J. Almolef, K. Faegri, K. Korsell, J. Comput. Chem. vol 3. p385 (1982). >> PS. The energy obtained from GAMESS is always lower than from >> Gaussian. Therefore, I believe that the speed is gained >> at the sacrifice of some precision. I think your mention about one point calculation. Gaussian use loose conversion threshold, 10**(-4). We get same energy on Gaussian and GAMESS(HONDO). Best regards. Akinori Murakami Mitsubishi Chemical Corporation